Structure of PDB 4njk Chain A Binding Site BS02

Receptor Information

>4njk Chain A (length=209) Species: 395019 (Burkholderia multivorans ATCC 17616)

TYAVKEIFYTLQGEGANAGRPAVFCRFAGCNLWSGREEDRAQAVCRFCDT
DFVGTDGENGGKFKDADALVATIAGLWPAGEAHRFVVCTGGEPMLQLDQP
LVDALHAAGFGIAIETNGSLPVLESIDWICVSPKADAPLVVTKGNELKVV
IPQDNQRLADYAKLDFEYFLVQPMDGPSRDLNTKLAIDWCKRHPQWRLSM
QTHKYLNIP

Ligand information

• Ligand ID: SAM
• InChI: InChI=1S/C15H22N6O5S/c1-27(3-2-7(16)15(24)25)4-8-10(22)11(23)14(26-8)21-6-20-9-12(17)18-5-19-13(9)21/h5-8,10-11,14,22-23H,2-4,16H2,1H3,(H2-,17,18,19,24,25)/t7-,8+,10+,11+,14+,27-/m0/s1
• InChIKey: MEFKEPWMEQBLKI-FCKMPRQPSA-N
• SMILES:
  CACTVS 3.341: C[S@@+](CC[C@H](N)C([O-])=O)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
  OpenEye OEToolkits 1.5.0: C[S+](CCC(C(=O)[O-])N)CC1C(C(C(O1)n2cnc3c2ncnc3N)O)O
  CACTVS 3.341: C[S+](CC[CH](N)C([O-])=O)C[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
  OpenEye OEToolkits 1.5.0: C[S@@+](CC[C@@H](C(=O)[O-])N)C[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O
  ACDLabs 10.04: [O-]C(=O)C(N)CC[S+](C)CC3OC(n2cnc1c(ncnc12)N)C(O)C3O
• Formula: C15 H22 N6 O5 S
• Name: S-ADENOSYLMETHIONINE
• ChEMBL: CHEMBL1235831
• PDB chain: 4njk Chain A Residue 302

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4njk Radical SAM enzyme QueE defines a new minimal core fold and metal-dependent mechanism.
• Resolution: 1.911 Å
• Binding residue (original residue number in PDB): F48 C49 D50 T51 T90 G91 G92 E93 E116 T117 N118 S133 K135 V151 M175 D176 Q202
• Binding residue (residue number reindexed from 1): F47 C48 D49 T50 T89 G90 G91 E92 E115 T116 N117 S132 K134 V150 M174 D175 Q201
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): F25 C31 C46 C49 D50 T51 E116 H204
• Catalytic site (residue number reindexed from 1): F24 C30 C45 C48 D49 T50 E115 H203
• Enzyme Commision number: 4.3.99.3: 7-carboxy-7-deazaguanine synthase.

Gene Ontology

Molecular Function

• GO:0000287 magnesium ion binding
• GO:0003824 catalytic activity
• GO:0016829 lyase activity
• GO:0016840 carbon-nitrogen lyase activity
• GO:0042802 identical protein binding
• GO:0042803 protein homodimerization activity
• GO:0046872 metal ion binding
• GO:0051536 iron-sulfur cluster binding
• GO:0051539 4 iron, 4 sulfur cluster binding
• GO:1904047 S-adenosyl-L-methionine binding

Biological Process

• GO:0008616 queuosine biosynthetic process

External links

• PDB: RCSB:4njk, PDBe:4njk, PDBj:4njk
• PDBsum: 4njk
• PubMed: 24362703
• UniProt: A0A0H3KB22|QUEE_BURM1 7-carboxy-7-deazaguanine synthase (Gene Name=queE)